Research workbench
X-ray structure of the M205W mutant of glic in complex with bromoform
Analyse X-ray structure of the M205W mutant of glic in complex with bromoform in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MZQ
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proton-gated ion channel
- UniProt
- Q7NDN8
- Ligands
- D12, PC8, 2IL, MBR, NA, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 37% helix, 34% strand | Q7NDN8 |
Ligands and binding sites
- D12 · Dodecane · ligand · 11 copies · chains A, B, E, C, D
- PC8 · 1,2-dioctanoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, B, C, D, E
- 2IL · (3R)-3-(dodecanoyloxy)tetradecanoic acid · ligand · 5 copies · chains A, B, C, D, E
- MBR · Tribromomethane · ligand · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 10 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.80 | 0.81 | 58 | D12, NA |
| 2 | 547 | 0.78 | 0.84 | 65 | MBR |
| 3 | 402 | 0.74 | 0.84 | 48 | empty |
| 4 | 389 | 0.73 | 0.84 | 50 | empty |
| 5 | 392 | 0.72 | 0.83 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2315 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 2296 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2295 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 2277 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2273 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5MZQ · X-ray structure of the M205W mutant of GLIC in complex with bromoform · the same entry in another collection · chain E against E, TM-score 1.00
- Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain D against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q7NDN8
- Elsewhere: RCSB PDB 5MZQ · PDBe 5MZQ · UniProt Q7NDN8
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